In all bacteria as well as mitochondria and chloroplasts the initiation of protein synthesis normally requires an N-formylated methionine residue. The special initiation tRNA, tRNAfMet, is charged with methionine by the Methionyl-tRNA synthetase (EC 6.1.10) which adds a methionine to either of the methionine tRNAs with the consumption of ATP. The formyl group is added to the charged tRNAfMet from 10-formyltetraydrofolate which is catalyzed by methionine-tRNAfMet formyl-transferase (EC 2.1.2.9). The formylated tRNA is transferred to the ribosome where protein synthesis is initiated (FIG. 1). All nascent polypeptides are synthesized with N-formyl methionine at the n-terminus.
Mature proteins do not by and large retain n-formyl methionine at the n-terminus. In fact, a rather heterogenous population of amino acids are normally found at the n-terminus of mature proteins—alanine, glycine, serine, threonine, or methionine. Larger amino acids are rarely found, which suggests that multiple catabolic processing might occur after or in concert with protein synthesis. All known amino-terminal peptidases cannot use formylated peptides as substrates. After translation, the formyl group is removed by Peptide Deformylase (pdf) as illustrated in FIG. 2. This metalloenzyme (EC 3.5.1.27) removes the formyl group from the peptide amino-terminus and releases the protein for possible further processing by methionine aminopeptidase (MAP; EC 3.4.11.18). The formylation/deformylation cycle is unique to eubacteria and does not occur in eucaryotic protein synthesis. The essential deformylation activity of pdf makes it an attractive target for crystallization and structural studies. Such studies may lead to the design of new antibiotics.